Computational protocol: Insights from the predicted interactions of plant derived compounds to the gluco-corticoid receptor as an alternative to dexa-methasone

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Protocol publication

[…] The information about ligand molecules for docking simulation Taraxterol (TARA), Beta-amyrin (BAMA), Alpha-amyrin (AAMA) Beta-sitosterol (SITO) and Stigmasterol (STIG) of Calotropis sp. and Amarogentin (AMAR), Amaroswerin (ASWE), Gentianine (GENT), Swerchirin (SWER), Swertiamarin (SAMA), Xanthone (XANT), Mangiferin (MANG) and Syringaresinol (SYRI) of S. Chiraytia were downloaded from PubChem chemical database of NCBI ( []. The 3D coordinate file of the GR (1M2Z) was retrieved from the Protein Data Bank (PDB). The Docking simulation was carried out using AutoDock 4.0 suite []. Before docking, the protein structures file was cleaned, removing the H2O molecules and HETATM, and then H-atoms were added to the target protein to attain correct ionization and tautomeric states of amino acid residues. Further, Gasteiger charges were added to the receptor molecule. The ligands to be docked were kept flexible, so as to explore number of torsional degrees of freedom in addition to the translational and rotational parameters. The rigid roots of each ligand were defined automatically; all rotatable dihedrals in the ligands were allowed to rotate freely. The required precalculated grid map was prepared covering the chain A of 1M2Z (1M2Z: A). To prepare, run and analyze the docking simulation the GUI program AutoDockTools (ADT) was used. The Lamarckian Genetic Algorithm (LGA) was chosen to search for the best conformers. During the docking process, a maximum of 10 conformers was considered for each compound. The population size was set to 150 and the individuals were initialized randomly. Maximum number of energy evaluation was set to 2500000, maximum number of generations 1000, maximum number of top individual the automatically survived set to 1, mutation rate of 0.02, crossover rate of 0.8, step sizes were 0.2 Å for translations, 5.0 for quaternions and 5.0 for torsions. Cluster tolerance 0.5Å, external grid energy 1000.0 max initial energy 0.0 max number of retries 100000 and 10 LGA runs were performed. All the AutoDock docking runs were performed in Intel Pentium vostro 1510 3.0 GHz of Dell with 1GB RAM. AutoDock 4.0 was compiled and run under Ubuntu 11.10 OS. Before docking of the compounds of C. gigantia and S. chirata, the 1M2Z chain was first docked using DEX ligand after removal of the existing bound ligand, so as to acertain whether the parameters used for study are satifactory. The ADME toxicity and other descriptors of the compounds were explored using online softwares Molinspiration, Osiris and FAFDrug2 [–]. […]

Pipeline specifications

Software tools AutoDock, Molinspiration
Applications Drug design, Protein interaction analysis
Diseases Asthma, Hyperlipoproteinemia Type II, Hypersensitivity
Chemicals Dexamethasone